Abstract: The Chaotianmen to Fuling reach in the fluctuating backwater area of the Three Gorges Reservoir is located within the National Germplasm Resource Protection Area for the four major Chinese carps in the upper Yangtze River. During the impoundment period of the Three Gorges Reservoir, the water depth is large and the flow velocity is low, which is suitable for the survival of the four major Chinese carps. During the drawdown and flood seasons of the Three Gorges Reservoir, the river channel restores its natural fluvial characteristics, characterized by reduced water depth and increased flow velocity, thereby narrowing the scope of suitable habitats for the four major Chinese carps. The meandering braided reaches in the fluctuating backwater area of the Three Gorges Reservoir feature distinctive geomorphic characteristics: after sharp bends, the river channel often widens and branches, with numerous stone ridges distributed at intervals along the nearshore area. This provides a natural topographic foundation for the creation of continuous shallow-bar and deep-pool habitats. During reef-clearing and spoil disposal operations in this river section, the waste spoil is often placed in nearshore deep-pool areas, which has a certain impact on the habitats of the four major Chinese carps. To address this issue, relying on the 4.5 m-depth waterway project from Chaotianmen to Fuling in the fluctuating backwater area of the Three Gorges Reservoir, and taking the Dajiantan meandering braided reach as a typical case, a scheme was proposed to create habitats for the four major Chinese carps using the reef-clearing spoil from the waterway regulation project. A 2D hydrodynamic model of the project reach was established and validated using MIKE21, and the hydrodynamic distributions under different hydrological conditions were calculated. Based on the Habitat Suitability Index (HSI) model, water depth and flow velocity were selected as key influencing factors to analyze the improvement effect of the shallow-bar and deep-pool habitat creation scheme in the meandering braided reach on the hydrodynamic conditions for the four major Chinese carps. The results show that in the meandering braided reaches of the fluctuating backwater area of the Three Gorges Reservoir, habitat creation using shallow bars can increase the HSI by up to 0.4 compared with the pre-project condition. This significantly improves the habitat quality for the four major Chinese carps during the drawdown and flood seasons and can provide a reference for habitat restoration in similar river reaches.